Campaign 2017 (PhD Chapter 1)


This series of files compile all analyses done during Chapter 1 for the regional campaign of 2017.

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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Caracteristics of each campaign

2014 2017 2017
Sampling date August-September June to August July
Criteria for perturbation Potentially impacted if close to the city or industries, References outside the bay Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered BSI BSI, CPC, BDA, MR BSI, MR
Number of sampled stations 40 (20 HI, 20 R) 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) 126 (111 BSI, 15 MR)
Parameters sampled Organic matter yes yes yes
Photosynthetic pigments no yes yes
Sediment grain-size yes yes yes
Heavy-metals yes yes (for a limited number of stations) no (interpolated based on 2014 and 2017 values)
Benthic communities Compartment targeted Macro-infauna Macro-infauna Macro-infauna
Sieved used 500 µm 1 mm 500 µm and 1 mm
Conservation technique Formaldehyle Formaldehyle Formaldehyle
Others N.A. N.A. N.A.

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

We only considered 500 µm communities for these analyses. Abundances of Bipalponephtys neotena (Bneo) and Nematoda (Nema) were also considered (see IndVal and SIMPER results).

Heavy metal concentrations for campaign 2017 have been kriged from the values collected at campaigns 2014 and 2016. As data is missing for metal concentrations outside BSI, two Designs have been used:

Statistics for each variable considered:

BSI, MR (without heavy metals)
  Mean SD SE Median Min Max 95% CI
depth 22.364 18.168 2.909 20.900 1.600 66.900 5.702
om 0.885 0.726 0.116 0.620 0.186 3.872 0.228
gravel 0.028 0.115 0.018 0.000 0.000 0.701 0.036
sand 0.649 0.271 0.043 0.675 0.005 0.992 0.085
silt 0.304 0.239 0.038 0.322 0.007 0.869 0.075
clay 0.020 0.084 0.014 0.000 0.000 0.407 0.026
S_500 10.436 4.994 0.800 11.000 1.000 23.000 1.567
N_500 79.795 80.331 12.863 58.000 1.000 382.000 25.212
H_500 1.588 0.620 0.099 1.643 0.000 2.568 0.194
J_500 0.700 0.210 0.034 0.738 0.000 1.000 0.066
BSI (only heavy metals)
  Mean SD SE Median Min Max 95% CI
arsenic 3.908 3.085 0.630 2.750 1.500 16.000 1.234
cadmium 0.150 0.041 0.008 0.145 0.090 0.230 0.017
chromium 55.163 20.949 4.276 54.750 28.000 110.700 8.381
copper 11.121 6.686 1.365 8.950 2.900 28.700 2.675
iron 49908.033 13633.036 2782.832 48883.150 28355.900 78471.300 5454.250
manganese 952.654 455.270 92.932 847.700 423.100 2098.000 182.142
mercury 0.024 0.016 0.003 0.021 0.008 0.087 0.006
lead 5.533 2.520 0.514 5.050 2.400 12.100 1.008
zinc 61.654 25.066 5.117 55.750 33.500 141.000 10.028

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Species richness

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

Regions

Organic matter

Grain-size

Species abundances

Diversity indices

Depth classes

Organic matter

Grain-size

Species abundances

Diversity indices

2.2. Phylum frequencies

Phylum abundances by condition
Phylum HI R
Arthropoda 879 81
Annelida 811 40
Mollusca 337 310
Nematoda 242 270
Echinodermata 29 104
Nemertea 4 0
Bryozoa 0 0
Chaetognatha 0 0
Cnidaria 0 3
Hemichordata 0 0
Phoronida 0 0
Platyhelminthes 0 0
Sipuncula 0 2

2.3. Species estimation curves

2.4. Principal Component Analysis

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

2.5. Non-metric Multidimensional Scaling

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

Species

Stations with no species were deleted from this analysis.

2.6. Hierarchical Agglomerative Clustering

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

## 127 132 139 154 156 171 176 177 186 187 188 193 194 195 196 197 198 206 211 221 228 230 231 236 243 246 248 249 251 252 254 255 
##   1   1   1   1   1   2   1   1   1   2   1   1   1   2   1   1   2   1   2   1   1   2   1   1   3   2   2   3   2   3   2   2 
## 257 258 260 261 264 267 270 
##   2   2   2   2   2   1   1

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

## 127 132 139 154 156 171 176 177 186 187 188 193 194 195 196 197 198 206 211 221 228 230 231 236 
##   1   1   2   2   2   3   3   2   3   3   3   1   1   3   2   2   2   3   3   3   2   3   2   2

Species

Stations with no species were deleted from this analysis.

## 127 132 139 154 156 171 176 177 186 187 188 193 194 195 196 197 198 206 211 221 228 230 231 236 243 246 248 249 251 252 254 255 
##   1   1   1   1   1   1   1   1   1   2   2   1   1   2   1   1   1   1   1   1   2   2   1   1   2   2   2   2   2   2   2   2 
## 257 258 260 261 264 267 270 
##   2   2   2   2   2   2   2


Elliot Dreujou

2020-01-20